Table S1.

CDE Sequences and Globin Reporter mRNA Half-Lives in NIH3T3 Cells, Related to Figures 1 and 2
Construct

t1/2 SD (hrs)

TNF-CDE37-V2

AGATCCTTCAGACAGACATGTTTTCTGTGAAAACGGAGCTGAGCTAGATCT

Sequence

8.8 2.2

TNF-CDE37-V3

AGATCCAGTTCAGACAGACATGTTTTCTGTGAAAACGGAGCTGAGCTAGATCT

1.4 0.5

human TNF-CDE37-V3

AGATCCTGTTGGCTCAGACATGTTTTCCGTGAAAACGGAGCTGAACAAGATCT

2.0 0.7

TNF-CDE37-V3-M1

AGATCCAGTTCAGA--------TTTTCTGTGAAAACGGAGCTGAGCTAGATCT

> 9.0*

TNF-CDE37-V3-M2

AGATCCAGTTCAGACAGACATGTTT--------------GCTGAGCTAGATCT

> 9.0*

TNF-CDE37-V3-M3

AGATCCAGTAGTGACAGACATGTTTTCTGTGAAAACGGAGCTGAGCTAGATCT

1.5 0.1

TNF-CDE37-V3-M4

AGATCCAGTTCAGACAGACATGTTTTCTGTGAAAACGGAGCACTGCTAGATCT

2.5 0.3

TNF-CDE37-V3-M5

AGATCCAGTAGTGACAGACATGTTTTCTGTGAAAACGGAGCACTGCTAGATCT

1.1*

TNF-CDE37-V3-M6

AGATCCAGTTCAGAGTGACATGTTTTCTGTGAAAACGGAGCTGAGCTAGATCT

1.4 0.4

TNF-CDE37-V3-M7

AGATCCAGTTCAGACAGACAACTTTTCTGTGAAAACGGAGCTGAGCTAGATCT

> 9.0

TNF-CDE37-V3-M8

AGATCCAGTTCAGAGTGACAACTTTTCTGTGAAAACGGAGCTGAGCTAGATCT

> 9.0*

TNF-CDE37-V3-M9

AGATCCAGTTCAGACAGACATGTTTAGGCTGAAAACGGAGCTGAGCTAGATCT

> 9.0

TNF-CDE37-V3-M10

AGATCCAGTTCAGACAGACATGTTTTCTGTGAAAAGTCTGCTGAGCTAGATCT

> 9.0*

TNF-CDE37-V3-M11

AGATCCAGTTCAGACAGACATGTTTAGGCTGAAAAGTCTGCTGAGCTAGATCT

> 9.0*

TNF-CDE37-V3-M12

AGATCCAGTTCAGACAGACATGTTTTCTGTGAAAACGCTGCTGAGCTAGATCT

1.3 0.2

TNF-CDE37-V3-M13

AGATCCAGTTCAGACAGACATGTTTAGTGTGAAAACGCTGCTGAGCTAGATCT

> 9.0

TNF-CDE37-V3-M14

AGATCCAGTTCAGACAGACATGTTTTCTGTGAAAAGTGAGCTGAGCTAGATCT

> 9.0

TNF-CDE37-V3-M15

AGATCCAGTTCAGACAGACATGTTTTCGCTGAAAAGTGAGCTGAGCTAGATCT

> 9.0

TNF-CDE37-V3-M16

AGATCCAGTTCAGACAGACATGTTTTCTGTGAAATGGGAGCTGAGCTAGATCT

> 9.0

TNF-CDE37-V3-M17

AGATCCAGTTCAGACAGACATGTTTTCTCAGAAATGGGAGCTGAGCTAGATCT

> 9.0

TNF-CDE37-V3-M18

AGATCCAGTTCAGACAGAGTTGTTTTCTGTGAAAACGGAGCTGAGCTAGATCT

2.0 0.7

TNF-CDE37-V3-M19

AGATCCAGTTCAGACAGACATCATTTCTGTGAAAACGGAGCTGAGCTAGATCT

> 9.0

TNF-CDE37-V3-M20

AGATCCAGTTCAGACAGACATCATTTCTGTGAAATGGGAGCTGAGCTAGATCT

2.7 0.8

TNF-CDE37-V3-M21

AGATCCAGTTCAGACAGACATGTTTAGTGTGAAAACGGAGCTGAGCTAGATCT

> 9.0

TNF-CDE37-V3-M22

AGATCCAGTTCAGACAGACATGTTTTCTGTCTAAACGGAGCTGAGCTAGATCT

> 9.0

TNF-CDE37-V3-M23

AGATCCAGTTCAGACAGACATGTTTAGTGTCTAAACGGAGCTGAGCTAGATCT

> 9.0

TNF-CDE37-V3-M24

AGATCCAGTTCAGACAGACATGTTTTCTATGAAAACGGAGCTGAGCTAGATCT

2.2 0.4

TNF-CDE37-V3-M25

AGATCCAGTTCAGACAGACATGTTTTCACAGAAAACGGAGCTGAGCTAGATCT

> 9.0

TNF-CDE37-V3-M26

AGATCCAGTTCAGACAGACATGTATTCTGTGAATACGGAGCTGAGCTAGATCT

5.0 0.8

TNF-CDE37-V3-M27

AGATCCAGTTCAGACAGACATGTTATCTGTGATAACGGAGCTGAGCTAGATCT

> 9.0

TNF-CDE17-ds

AGATCCAGTGTTTTCTGTGAAAACGCTAGATCT

> 9.0

TNF-CDE17-ss

TCTAGATGTTTTCTGTGAAAACGACCGGT

1.1 0.4

4.8 2.5

5.6 1.1

> 9.0

5.6 2.5

ICOS-CDE17-ss
TNF-CDE150
TNF-CDE150-M16
TNF-CDE150-M20

XXX
XXX
XXX
--XXX
XXX
XXX
*

TCTAGAAAATTTCTGTGAAATAAACCGGT
AGATCCTTTGGAAGGCCGGGGTGTCCTGGAGGACCCAGTGTGGGAAGCTGTCTTCAGACAG
ACATGTTTTCTGTGAAAACGGAGCTGAGCTGTCCCCACCTGGCCTCTCTACCTTGTTGCCT
CCTCTTTTGCTTATGTTTAAAACAAAATATTTATAGATCT
AGATCCTTTGGAAGGCCGGGGTGTCCTGGAGGACCCAGTGTGGGAAGCTGTCTTCAGACAG
ACATGTTTTCTGTGAAATGGGAGCTGAGCTGTCCCCACCTGGCCTCTCTACCTTGTTGCCT
CCTCTTTTGCTTATGTTTAAAACAAAATATTTATAGATCT
AGATCCTTTGGAAGGCCGGGGTGTCCTGGAGGACCCAGTGTGGGAAGCTGTCTTCAGACAG
ACATCATTTCTGTGAAATGGGAGCTGAGCTGTCCCCACCTGGCCTCTCTACCTTGTTGCCT
CCTCTTTTGCTTATGTTTAAAACAAAATATTTATAGATCT

CDE sequence
nucleotides introduced into cloning context
mutation
deletion
cloning sites
flanking TNF 3UTR sequence in CDE150
primer sites
mRNA half-lives determined upon stable transfection

Table S2. Proteins Enriched by CDE RNA Affinity Purification, Related to Figure 3
Name

Symbol

No of Peptides

MW
(kDa)

4xS1m

CDE-4xS1m

Roquin, RING finger and CCCH zinc finger protein 1

Rc3h1

125

Cleavage and polyadenylation specificity factor subunit 7

Cpsf7

52

Ribosome biogenesis regulatory protein homolog

Rrs1

42

Roquin2, RING finger and CCCH zinc finger protein 2

Rc3h2

131

Nucleophosmin

Npm

33

Splicing factor, proline- and glutamine-rich

Sfpq

75

Fragile X mental retardation syndrome-related protein 1

Fxr1

76

Table S3. Proteins Purified with Roquin and Roquin2, Related to Figure 5
Protein

MW (kDa)

No of peptides
EGFP

EGFP-Roquin

EGFP-Roquin2

CNOT1 = Not1

267

75

68

RC3H1 = Roquin

126

28

11

PABP1

71

24

20

TAB182 = TNKS1BP1

182

19

IF2B3

64

17

RC3H2 = Roquin2

132

12

45

PHB2

33

12

10

GBLP

35

12

YBOX1

36

12

HNRPM

78

12

IF2B1

63

12

MOV10

114

RCD1 = Not9

34

PABP4

71

STML2

39

PDIA1

57

DHX30

134

DBPA

40

CNOTA = Not10

82

HNRPC

34

P5CR2

34

CNOT2 = Not2

60

DDX21

87

VIME

54

CB029

55

PAIRB

45

AGAL

49

IF2B2

66

LARP1

124

KCRB

43

KPYM

58

CNOT3 = Not3

82

RENT1

124

AFG32

89

ZCHC3

44

AL7A1

58

PCBP2

39

ILF2

43

PDIA6

48

DHB4

80

RBMX

42

DDX3X

73

AAAT

57

CNO6L = Ccr4b

63

CNOT8 = Caf1b

34

CNOT7 = Caf1a

33

Blue: bait proteins

Yellow: proteins of the Ccr4-Caf1-Not complex

Table S4. Bioinformatics Prediction of CDEs in Mouse 3 UTRs, Related to Figure 6

Name

GeneID

Bmpr1a

12166

Fos

Genomic Coordinates

CDE Sequence*

Stem (nt)

Conservation

chr14(-):35227347-35227367

GCTTTCTGTGAAAGC

41

14281

chr12(+):86818025-86818045

GTTTTCCATGAAAAC

40

D11Wsu99e

28081

chr11(-):113524586-113524606

CCTTCTGTGAAGG

38

Pdia6

71853

chr12(+):17290969-17290989

AATTCTATGAATT

38

Prkg1

19091

chr19(-):30639725-30639745

CATTTCTGTGAAATG

38

Fbxo11

225055

chr17(-):88390771-88390791

TCTTTCTATGAAAGA

38

Slc25a25

227731

chr2(-):32271585-32271605

CATTCTGTGAATG

37

Brwd1

93871

chr16(-):96223705-96223725

TTTTCTATGAAAA

36

Nfkbiz

80859

chr16(-):55812724-55812744

TTGTTTCTATGAAACAA

36

Epc1

13831

chr18(-):6436103-6436123

TCTCTTCTGTGAAGAGA

36

Adamts6

108154

chr13(+):105283940-105283960

ACTTCTGTGAAGT

36

Baz2b

407823

chr2(-):59738167-59738187

TTTTCTGTGAAAA

36

Kpna4

16649

chr3(-):68876833-68876853

TTTTCTATGAAAA

35

Dscaml1

114873

chr9(+):45561741-45561761

TTTTTCTATGAAAAA

35

Bptf

207165

chr11(-):106896548-106896568

CTTTCTATGAAAG

35

Rc3h2

319817

chr2(-):37229326-37229346

AACTTCTGTGAAGTT

34

Lpin2

64898

chr17(+):71598326-71598346

TCTTTCTGTGAAAGA

34

Hmgxb3

106894

chr18(-):61291103-61291123

CCCTTCTGTGAAGGG

34

Slc35f4

75288

chr14(-):49918345-49918365

TATATTCTGTGAATATA

34

4931408A02Rik

70967

chr16(+):90904812-90904832

CCTTCTGTGAAGG

34

Frmd6

319710

chr12(+):72003070-72003090

TCCTTTCTGTGAAAGGA

34

Rc3h1

381305

chr1(+):162901788-162901808

AACTTCTGTGAAGTT

34

Phf13

230936

chr4(-):151363771-151363791

GTTTCTGTGAAAC

33

Edem3

66967

chr1(+):153668882-153668902

CATTCTGTGAATG

33

Tnf

21926

chr17(-):35336527-35336547

GTTTTCTGTGAAAAC

33

Aggf1

66549

chr13(-):96120915-96120935

TTCTTCTGTGAAGAA

33

Uhrf1bp1

224648

chr17(+):28036936-28036956

TGGTTCTGTGAACCA

33

Ctla4

12477

chr1(+):60972606-60972626

ATTTTCCATGAAAAT

32

Lpin1

14245

chr12(-):16543793-16543813

TCTTTCTGTGAAAGA

32

Prkd1

18760

chr12(-):51442550-51442570

TGTTCTATGAACA

32

Gramd3

107022

chr18(+):56663304-56663324

CATTTCTATGAAATG

32

Crispld2

78892

chr8(+):122576557-122576577

TTTTTCTATGAAAAA

31

Plag1

56711

chr4(-):3828830-3828850

GTTTCTATGAAAC

31

Mdga2

320772

chr12(-):67567952-67567972

TTTTCTGTGAAAA

30

Wnt3a

22416

chr11(-):59061599-59061619

TTTCTTTCTATGAAAGAAA

30

Rbbp5

213464

chr1(+):134401367-134401387

CCTTTCTGTGAAAGG

28

Slc25a14

20523

chrX(+):46015298-46015318

TCTTCTGTGAAGA

28

Scmh1

29871

chr4(+):120201987-120202007

GTCCTTCCATGAAGGAC

27

Efna4

13639

chr3(-):89137749-89137769

GTCTTCTGTGAAGAC

27

Icos

54167

chr1(+):61056327-61056347

ATTTCTGTGAAAT

26

Atp2b1

67972

chr10(+):98488582-98488602

ATTTCTGTGAAAT

26

Ppp1r10

52040

chr17(+):36069089-36069109

TGTTTTCTATGAAAACA

26

Nfkbid

243910

chr7(+):31213418-31213438

GATTTCTGTGAAATC

25

Bcan

12032

chr3(-):87796498-87796518

TACTTCTGTGAAGTA

25

Nfkbid

243910

chr7(+):31213446-31213466

TGTTTCTGTGAAACA

23

Sertad3

170742

chr7(+):28261918-28261938

CCTTCCGTGAAGG

23

Pdzk1ip1

67182

chr4(+):114766430-114766450

TTATTTCTGTGAAATAA

21

Ier3

15937

chr17(+):35959816-35959836

TGTTCTGTGAACA

21

Agap2

216439

chr10(+):126529456-126529476

CCCTTTCCGTGAAAGGG

20

Kctd8

243043

chr5(-):69500797-69500817

ATTTCTGTGAAAT

20

Shprh

268281

chr10(+):10934277-10934297

TCTTCTGTGAAGA

20

Pex12

103737

chr11(-):83108689-83108709

GTTTCTATGAAAC

19

Prr3

75210

chr17(-):36109634-36109654

TGTTTTCTGTGAAAACA

19

Zfp82

330502

chr7(-):30841131-30841151

AACATTCTGTGAATGTT

15

Fam188b

330323

chr6(+):55268443-55268463

CCTTCCATGAAGG

13

Chic1

12212

chrX(+):100587042-100587062

TTGTTTCCATGAAACAA

11

Dcaf12

68970

chr4(-):41239674-41239694

ACTTTCTGTGAAAGT

Rps15a

267019

chr7(-):125248827-125248847

CATTTCTGTGAAATG

Fam63b

235461

chr9(-):70447133-70447153

ATTTCTGTGAAAT

Cdc14a

229776

chr3(-):115975784-115975804

TGTTCTATGAACA

Hes5

15208

chr4(+):154336042-154336062

ACTTCTGCGAAGT

1700021K19Rik

100502698

chr16(-):32822768-32822788

AGTTCTGTGAACT

Hdx

245596

chrX(-):108689838-108689858

TATTCTATGAATA

Arhgef26

622434

chr3(+):62264708-62264728

CTTTCTACGAAAG

Tnks2

74493

chr19(+):36966493-36966513

CTTTCCATGAAAG

Tcf12

21406

chr9(-):71693792-71693812

ATTTCCATGAAAT

Tmem123

71929

chr9(+):7792315-7792335

TATTCCATGAATA

Dagla

269060

chr19(-):10319815-10319835

TATTCTATGAATA

Ifi205

226695

chr1(-):175942182-175942202

TTTTCTATGAAAA

Pxdn

69675

chr12(+):30702022-30702042

ACTTCTGTGAAGT

C330018D20Rik

77422

chr18(-):57116623-57116643

AGTTCTGTGAACT

Gpr30

76854

chr5(+):139903599-139903619

CCTTCCGTGAAGG

Steap3

68428

chr1(-):122123516-122123536

CCTTCTGCGAAGG

Pak1

18479

chr7(+):105059961-105059981

CTGTTTCTACGAAACAG

Sftpb

20388

chr6(+):72264314-72264334

ATTTCTATGAAAT

Yipf4

67864

chr17(+):74898673-74898693

TATTCCGCGAATA

Cnot1

234594

chr8(-):98243625-98243645

TGTTCCGTGAACA

Pkib

18768

chr10(+):57460174-57460194

TTTTCTATGAAAA

Homez

239099

chr14(-):55474962-55474982

ATTTCTATGAAAT

Gng12

14701

chr6(+):66968118-66968138

AAATTTCCGTGAAATTT

Gtf3c4

269252

chr2(-):28680536-28680556

ATTTCTGTGAAAT

Tdg

21665

chr10(+):82112588-82112608

TGTTCTGTGAACA

Fyco1

17281

chr9(-):123700645-123700665

CTTTCTATGAAAG

Kcnj6

16522

chr16(-):94982853-94982873

CTTTCTGTGAAAG

Rpusd4

71989

chr9(+):35083491-35083511

ATTTCTGTGAAAT

Msx2

17702

chr13(-):53562745-53562765

ATTTCTATGAAAT

D630042F21Rik

330428

chr6(+):129467527-129467547

TGTTCTGTGAACA

Lrrcc1

71710

chr3(+):14566932-14566952

CATTCCATGAATG

2810021B07Rik

66308

chr13(+):17790322-17790342

AGTTCTATGAACT

Mnda

381308

chr1(-):175826538-175826558

TTTTCTATGAAAA

Ccdc50

67501

chr16(+):27447812-27447832

CCTCCTTCTGCGAAGGAGG

Sh3bp2

24055

chr5(+):34906164-34906184

TTTTCTGTGAAAA

Pdcd6

18570

chr13(-):74440614-74440634

CAATTCTGTGAATTG

Slc27a4

26569

chr2(+):29672350-29672370

CTTTCTATGAAAG

Zfp111

56707

chr7(-):24978733-24978753

CTTTCTATGAAAG

BC027231

212547

chr16(+):44737321-44737341

TGTTTCTATGAAACA

Mndal

100040462

chr1(-):175787404-175787424

TTTTCTATGAAAA

Gvin1

74558

chr7(-):113043857-113043877

ATTTTCTATGAAAAT

Gm4070

100042856

chr7(-):113300274-113300294

ATTTTCTATGAAAAT

Mau2

74549

chr8(-):72541564-72541584

CCTTCTGTGAAGG

Dap3

65111

chr3(-):88726711-88726731

TTTTCTGTGAAAA

Slc7a12

140918

chr3(+):14505767-14505787

TTATTCTATGAATAA

Crispld1

83691

chr1(+):17756207-17756227

TTTTCCATGAAAA

Lrrtm4

243499

chr6(+):79974907-79974926

ACTTTCTATGAAAGT

1810008A18Rik

108707

chr10(-):76949401-76949421

GTTTCTGTGAAAC

Lilrb4

14728

chr10(+):51216088-51216108

CATTCCATGAATG

Gp49a

14727

chr10(+):51205809-51205829

CATTCCATGAATG

Zfp866

330788

chr8(-):72285798-72285818

ATTTCTGTGAAAT

Afg3l1

114896

chr8(+):126027479-126027499

CGTTCCGTGAACG

* Stem depicted in black, loop depicted in red

Number of species with a conserved CDE at this genomic position in the UCSC 46 vertebrate species alignment

Alignment at this genomic position was not available

Yellow: CDEs conserved in > 10/46 vertebrate species

Table S5. Functional Categories of Genes Containing Conserved 3 UTR CDEs, Related to Figure 6
Number of genes
Gene ontology term (biological process)
observed

expected

Regulation of developmental process

13

2.9

Transcription, DNA-dependent

18

5.7

Regulation of RNA metabolic process

18

5.8

RNA biosynthetic process

18

5.8

Nucleic acid metabolic process

21

8.0

Negative regulation of T-cell differentiation

0.05

Table S6. mRNAs Significantly Enriched by Roquin-IP, Related to Figure 6

fold enrichment
(Roquin-IP /
control-IP)

fold enrichment
(Roquin-IP /
input)

Name

GeneID

CDE

p-value
(Roquin-IP vs
control-IP)

Nfkbid

243910

3UTR, conserved (2)

2.1E-32

475.1

172.1

Tnf (TNF)

21926

3UTR, conserved

1.1E-09

191.8

120.2

Irf4

16364

1.7E-15

179.2

69.2

Gm527

217648

5.3E-20

179.0

114.0

D5Ertd579e

320661

ORF (2)

3.7E-36

112.4

131.1

Rc3h1 (Roquin)

381305

3UTR, conserved

1.8E-32

99.8

71.4

Tcf7l2

21416

6.7E-21

76.4

68.2

Csf3 (G-CSF)

12985

2.3E-03

72.8

45.4

Id1

15901

2.3E-04

71.6

122.2

Slc39a14

213053

8.6E-05

67.1

34.0

Zfp408

381410

4.6E-24

59.1

62.1

Calcrl

54598

7.3E-06

58.0

32.8

Rc3h2 (Roquin2)

319817

3UTR, conserved

6.0E-16

44.2

27.3

Ptger4

19219

8.0E-16

41.7

22.7

Ptpre

19267

4.6E-17

41.4

24.5
52.0

Id3

15903

2.1E-23

40.7

Mgat5

107895

5.8E-11

40.7

19.4

Adamts1

11504

2.3E-05

39.1

40.3

Clk1

12747

4.7E-19

33.4

6.3

Nfkbiz

80859

3UTR, conserved

4.9E-07

32.7

33.6

Ap1g1

11765

1.5E-09

31.7

29.8

Usp53

99526

6.4E-18

29.2

15.4

B630005N14Rik

101148

1.2E-16

29.1

30.6

Map3k8

26410

1.5E-16

28.2

16.4

Id2

15902

4.1E-03

27.7

13.2

Pex1

71382

1.1E-09

26.8

17.2

Smek2

104570

4.3E-16

26.5

14.0

4732418C07Rik

230648

1.0E-19

26.1

28.3

Bmpr1a

12166

3UTR, conserved

1.5E-16

26.1

22.5

Icos

54167

3UTR, conserved

1.7E-05

25.0

13.1

Zbtb43

71834

7.4E-15

24.5

18.5

Ier3

15937

3UTR, conserved

8.1E-04

24.0

30.6

Fbxo33

70611

1.9E-17

22.2

16.5

Pik3ca

18706

2.5E-05

21.7

20.4

Rybp

56353

6.4E-13

21.6

21.9

Tigd5

105734

1.1E-03

21.2

31.2

Ss18l1

269397

4.7E-05

21.1

5.2

Lfng

16848

5.6E-08

19.7

17.5

Pptc7

320717

4.1E-06

19.1

25.3
10.1

Rsf1

233532

1.8E-13

17.1

Lysmd4

75099

2.4E-03

16.8

5.4

Mlec

109154

4.7E-08

16.8

20.9

Fam160b1

226252

3.2E-13

16.5

11.0

D030056L22Rik

225995

7.9E-04

15.8

23.5

Sec24c

218811

2.5E-15

15.8

13.8

Tmem2

83921

4.6E-09

15.7

5.3

5830415F09Rik

74753

1.3E-09

15.1

19.8

Cenpf

108000

1.4E-03

15.0

7.3

Etaa1

68145

1.1E-12

14.8

11.5

Nedd1

17997

4.4E-13

14.8

10.5

Ipo11

76582

ORF (2)

9.3E-05

14.7

8.7

Ppan

235036

5.1E-06

14.7

13.1

Ppp1r10

52040

3UTR, conserved

2.1E-05

14.5

13.7

Tm2d3

68634

2.2E-03

14.5

11.6

Ndst2

17423

3.2E-12

14.3

14.8

Slc35e3

215436

3.6E-07

13.4

11.3

Prr3

75210

3UTR, conserved

5.6E-13

13.1

32.8

Agbl3

76223

1.2E-03

13.0

11.0

Msl2

77853

5.4E-06

12.4

12.4

Hinfp

102423

9.9E-09

12.3

6.9

Kctd6

71393

7.0E-08

11.9

33.3

Nuf2

66977

1.7E-12

11.9

6.8

Cgrrf1

68755

2.0E-07

11.8

7.8

Rbm33

381626

7.4E-12

11.2

7.8

Aggf1

66549

3UTR, conserved

3.7E-05

11.2

14.8

Pole2

18974

ORF

2.2E-06

11.0

10.4

Papolg

216578

2.3E-10

11.0

8.1

Tfap4

83383

9.2E-06

10.7

5.9

Fam76b

72826

1.3E-04

10.7

5.3

Cdc7

12545

5.3E-09

10.6

7.6

2410042D21Rik

72425

5.0E-08

10.4

12.2

Dnajc10

66861

1.8E-03

10.4

6.6

Cdon

57810

4.0E-03

10.3

4.5

Ap1s3

676051

2.1E-03

10.0

11.3

Nfxl1

100978

1.6E-08

9.9

7.9

Sacm1l

83493

7.3E-11

9.8

8.7

Zfp367

238673

1.8E-10

9.5

7.5

Hcst

23900

4.4E-05

9.4

9.4

Dcun1d1

114893

6.4E-06

9.3

5.8

Fbxo11

225055

3UTR, conserved

8.8E-09

9.3

5.7

B4galt5

56336

ORF

7.4E-10

8.9

10.4

Mthfd2

17768

1.6E-10

8.9

13.0

Mrps33

14548

4.4E-08

8.8

6.2

Rbbp5

213464

3UTR, conserved

2.9E-08

8.8

7.7

Ube2q2

109161

1.6E-06

8.7

7.2

0610030E20Rik

68364

1.9E-08

8.6

10.6

4732471D19Rik

319719

4.1E-08

8.6

7.8

Rabl2

68708

1.4E-04

8.5

6.3

Hmgxb3

106894

3UTR, conserved

1.6E-08

8.5

8.6

Lig4

319583

1.0E-03

8.4

4.9

Fam84b

399603

3.1E-08

8.2

8.5

Epc1

13831

3UTR, conserved

7.0E-04

8.1

9.3

Dpy19l4

381510

9.3E-05

8.1

AI597479

98404

9.8E-08

8.1

6.0

Pik3cb

74769

8.8E-09

8.0

8.4

Purple: mRNA significantly enriched by Roquin-IP that contains a conserved CDE in the 3UTR
Green: mRNA significantly enriched by Roquin-IP that contains a CDE in the ORF

8.0

Table S7. DNA Oligonucleotides, Related to Experimental Procedures

Name

Sequence

Description

G078

GGTGGTCGGAAAGCTATC
TTACAAAGTCACTCAGGATG
TTAAGCTAGCAGGGAATGGG

S7 probe F

GCCGATTTAGGTGACACTATAGAATACTGGCTCTGTGAGG
GTGCATCTGTCCAGTG
GCCGATTTAGGTGACACTATAGAATACCCTGAAGTTCTC
GCCGATTTAGGTGACACTATAGAATACTATAGACACCAG
GCCGATTTAGGTGACACTATAGAATACTTAGCGTCTTCG
AGGGGGCAGAAATTGATGGACGAT
TGGGTTCTGGGGCACTTTG
GAGCGGGCCGTGGTGTC
CTTGGCAATGTTGGGTTCCTC
TGCCTATGTCTCAGCCTCTTC
GAGGCCATTTGGGAACTTCT
ACTCCACTCACGGCAAATTCAACG
AAGACACCAGTAGACTCCACGACA
CAGGTGAACACCACGGATT
CTCACAGCTCCCTTCTGGAT
ATATTCGTGAACATAAAGGCAAGA
TCAGTGGCGTTAGGCTCTG
CCAAGTAATACGACTCACTATAGGCCTGGCTCACAAATACCACTG
AATTTTTGGCAGAGGGAAAAAG
CCAAGTAATACGACTCACTATAGGTTTGGAAGGCCGGGGT
ATAAATATTTTGTTTTAAACATAAGCAAAAGAG
CATGGCTGCAACACTTACACAGCA
ATTGCAAGCCAGTGCCAATACCTG
TTGTACCTGAAGCCACTCAGCAGT
TCCACTAGCTGGCAATGAACCAGA
TGCCCATTCTCAGGAAGAGCTTGA
GCTGTGGTTGTGACAGTGCTGTTT
CCCAAGCTTGATATCATCCACCATGGTGAGCAAG
TTAAGGTACCCTTGTACAGCTCGTCCATGCCGAG
TGGACACAGTATCATACCCAGAAAACACCTGTCTCTTCAACTCTTCCTGTGGCCA
GATCATCGATTCAGCTGTTAACCATCTTCCCA
GATCGGATCCTTTGGAAGGCCGGGGT
GATCAGATCTATAAATATTTTGTTTTAAACATAAGCAAAAGAG
TTCTGTGAAATGGGAGCTGAG
TTTCACAGAAAACATGTCTGTCTGA
GACAGACATCATTTCTGTGAAATGGGA
ATGTCTGTCTGAAGACAGCTTCC
AAACTAGTATGCGCCGAGATTTACGA
CATACTAGTTTTATACTTGCTGTTTGGCTG
GATCCAATTGTTTTGCAGCGAACTG
AACATACATGCGTCGAGATATGAAG

mouse TNF probe R

G083
G314
G316
G1000
G1001
G1008
G1009
G1706
G1707
G1712
G1713
G1844
G1845
G2053
G2054
G2181
G2182
G2199
G2200
G2234
G2235
G2332
G2333
G2364
G2365
G2392
G2393
G2394
G2395
G1612
G1613
G2421
G2427
G2495
G2496
G2497
G2498
G2501
G2502
G2554
G2555
G2556
G2576

Ncl probe R
mouse TNF probe F
globin probe R
globin probe F
S7 probe R
Ncl probe F
mouse Ncl qPCR F
mouse Ncl qPCR R
mouse Ier3 qPCR F
mouse Ier3 qPCR R
mouse TNF qPCR F
mouse TNF qPCR R
mouse Gapdh qPCR F
mouse Gapdh qPCR R
mouse Nfkbiz qPCR F
mouse Nfkbiz qPCR R
mouse Nfkbid qPCR F
mouse Nfkbid qPCR R
pT7-in-line F
in-line R
pT7-CDE150 mouse in-line F
CDE150 mouse in-line R
mouse Nupl1 qPCR F
mouse Nupl1 qPCR R
mouse Roquin qPCR F
mouse Roquin qPCR R
mouse Roquin2 qPCR F
mouse Roquin2 qPCR R
EGFP F, HindIII-EcoRV
EGFP R, KpnI
mouse Roquin2 cDNA F
mouse Roquin2-ClaI cDNA R
CDE150-BamHI-outF
CDE150-outR-BglII
CDE150-M16 F
CDE150-M16 R
CDE150-M20 F
CDE150-M20 R
Roquin2 cDNA C413R F
Roquin2 cDNA C413R R
Roquin2-MfeI cDNA F
Roquin cDNA C419R F

G2577
G2579
G2592
G2593
G2622
G2623
G2723
G2724
G2729
G2730
G2737
G2738
G2747
G2748
G2788
G2789
G2790
G2791
G2840
G2842
G2843
G2855
G2856

CATGTATGTTTTGTATTTGCTATGCTGT
GATCCACATGGTGGTGGAGTATAGTACATACC
TTCCCCCTGTTGAAGTTCC
CTTGCGAGTCAGCTGGTTG
GATACTGTGTCCACTGATCTGGC
TCATTTGCACAGAGTGTTCAGG
TGACCTGGGCCTAGCTGTTA
TTCAGGCTTTCATCCAGCA
CTCACATCCTGGACACTGGA
ACTGGGCTCCAGCTTCTGT
TGTTGGCCCTCTATGAATCTG
TGGAACCACAGACCACCTG
TTCATCGTATTGGAAGATCAGG
TTGGGATGGGTTTGATCTCT
AGGGACCGGTGTCGACC
AGAGCAATTGTTAGCTCCTGAACA
GTGACCGAACTGATTCTCCAGCACCAG
CAGTTCGGTCACTGTGCGTTCACCTAAAG
ATTAATCGATCTATTCCTGTGAATGTG
TTATACCGGTGGAACTGGAAAAG
GTCCCACGTGGAATCAGTTG
TTATACCGGTGCGCCCAATGCAGAGGAA
TATAATCGATGAGTAACTCCAAATGGGGTCTTAG

Roquin cDNA C419R R

Roquin-DraIII cDNA R
mouse Ppp1r10 qPCR F
mouse Ppp1r10 qPCR R
BstXI-Roquin2 cDNA R
Roquin-DraIII cDNA F
mouse Bmpr1a qPCR F
mouse Bmpr1a qPCR R
mouse Pdia6 qPCR F
mouse Pdia6 qPCR R
mouse Hmgxb3 qPCR F
mouse Hmgxb3 qPCR R
mouse Rck qPCR F
mouse Rck qPCR R
AgeI-SalI-Roquin flanking fr1 F
MfeI-Roquin flanking fr2 R
siRNA-resistant Roquin fr2 F
siRNA-resistant Roquin fr1 R
ClaI-Stop-N-term R
Roquin C-term F
Roquin C-term R
ROQ-AgeI F
ROQ-ClaI R